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Knowledge on the duration of Cryptosporidium oocyst shedding, and how shedding may be affected by subtypes and clinical parameters, is limited. Reduced transmission may be a secondary benefit of cryptosporidiosis treatment in high-prevalence areas. We conducted a prospective clinical case series in children of <5 years presenting with diarrhea to a health center and a hospital in Ethiopia over an 18-month period. Stool samples were collected repeatedly from children diagnosed with cryptosporidiosis for up to 60 days. Samples were examined, and Cryptosporidium shedding was quantified, using auramine phenol, immunofluorescent antibody staining, and quantitative PCR (qPCR). In addition, species determination and subtyping were used to attempt to distinguish between new infections and ongoing shedding. Duration and quantity of shedding over time were estimated by time-to-event and quantitative models (sex- and age-adjusted). We also explored how diarrheal severity, acute malnutrition, and Cryptosporidium subtypes correlated with temporal shedding patterns. From 53 confirmed cryptosporidiosis cases, a median of 4 (range 1 to 5) follow-up stool samples were collected and tested for Cryptosporidium. The median duration of oocyst shedding was 31 days (95% confidence interval [CI], 26 to 36 days) after onset of diarrhea, with similar estimates from the quantitative models (31 days, 95% CI 27 to 37 days). Genotype shift occurred in 5 cases (9%). A 10-fold drop in quantity occurred per week for the first 4 weeks. Prolonged oocyst shedding is common in a pediatric clinical population with cryptosporidiosis. We suggest that future intervention trials should evaluate both clinical efficacy and total parasite shedding duration as trial endpoints. IMPORTANCE Cryptosporidiosis is an important cause of diarrhea, malnutrition, and deaths in young children in low-income countries. The infection spreads from person to person. After infection, prolonged release of the Cryptosporidi

Background Cryptosporidiosis is a major cause of diarrhoea in young children in low-and-middle-income countries. New interventions should be informed by evidence pertaining to risk factors and their relative importance. Inconsistencies in the literature may to some extent be explained by choice of methodology, furthermore, most previous risk factor studies compared crypto-sporidiosis cases to diarrhoea cases of other aetiologies rather than with controls without diarrhoea. Methodology/Principal findings We investigated a broad set of factors in under-2-year-olds presenting with diarrhoea to a hospital and a health center in southwestern Ethiopia. We applied quantitative cut-offs to distinguish between cryptosporidiosis and incidental Cryptosporidium infection or carriage, a hierarchical causal framework to minimize confounding and overadjustment, and a case-case-control design, to describe risk factors for both cryptosporidiosis and non-cryptosporid-iosis diarrhoea. Moderate and severe acute malnutrition were strongly associated with both cryptosporidiosis and non-cryptosporidiosis diarrhoea. Previous healthcare attendance and low maternal education were only associated with cryptosporidiosis, whereas unsafe child stool disposal, prematurity and early cessation of exclusive breastfeeding were significantly associated with non-cryptosporidiosis diarrhoea only. By estimation of population attributable fractions, socioeconomic factors—specifically low maternal education—and public tap water use, were apparently more important risk factors for cryptosporidiosis than for non-cryptosporidiosis diarrhoea. Conclusions/Significance Nutritional management of moderate acute malnutrition may be an effective intervention against cryptosporidiosis, particularly if combined with targeted therapy for cryptosporidiosis which, again, may mitigate nutritional insult. Focused caregiver education in healthcare settings and follow-up of children with acute malnutrition may prevent or

Background: Cryptosporidiosis is a common cause of diarrhoea in young children (aged younger than 24 months) in low-resource settings but is currently challenging to diagnose. Light-emitting diode fluorescence microscopy with auramine-phenol staining (LED-AP), recommended for tuberculosis testing, can also detect Cryptosporidium species. A lateral-flow test not requiring refrigerator storage (by contrast with most immunochromatographic lateral-flow assays) has also recently been developed for Cryptosporidium spp detection. We aimed to evaluate the diagnostic accuracy and operational feasibility of LED-AP and the lateral-flow test strip for cryptosporidiosis in children. Methods: We did a prospective diagnostic accuracy study in two health-care facilities in Ethiopia, in a consecutive series of children younger than 5 years of age with diarrhoea (three or more loose stools within the previous 24 h) or dysentery (at least one loose stool with stains of blood within the previous 24 h). Stool samples were tested for Cryptosporidium spp by LED-AP and the lateral-flow test strip; accuracy of each test was estimated by independent and blind comparison with a composite reference standard comprising quantitative immunofluorescent antibody test (qIFAT), ELISA, and quantitative PCR (qPCR). Quantitative cutoff values for diarrhoea-associated infection were established in an embedded case-control substudy, with cases of cryptosporidiosis coming from the 15 districts in and around Jimma and the eight districts surrounding Serbo, and community controls without diarrhoea in the previous 48 h recruited by weekly frequency matching by geographical district of the household, age group, and enrolment week. Findings: Stool samples from 912 children with diarrhoea or dysentery and 706 controls from the case-control substudy were tested between Dec 22, 2016, and July 6, 2018. Estimated reference-standard cutoff values for cryptosporidiosis positivity were 2·3 × 105 DNA copie